Status
This draft release was produced using Illumina data and wgsim simulated read pairs using Newbler assembly as reference. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.
Summary statistics for the Phlebiopsis gigantea 11061_1
CR5-6 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 30.14 |
| Sequencing read coverage depth | 144.9 |
| # of contigs | 1195 |
| # of scaffolds | 573 |
| # of scaffolds >= 2Kbp | 506 |
| Scaffold N50 | 72 |
| Scaffold L50 (Mbp) | 0.12 |
| # of gaps | 622 |
| % of scaffold length in gaps | 1.5% |
| Three largest Scaffolds (Mbp) | 0.61, 0.54, 0.46 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 42986 | 17915 | 41.7% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1714 | 1459 |
| transcript | 1380 | 1164 |
| exon | 230 | 145 |
| intron | 69 | 56 |
| description: | ||
| protein length (aa) | 411 | 338 |
| exons per gene | 6.00 | 5 |
| # of gene models | 11891 |
Collaborators
- PI: Dan Cullen, USDA Forest Products Laboratory
- David Hibbett, Clark University
- Igor Grigoriev, DOE Joint Genome Institute
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Dueñas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutiérrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kües U, Berka RM, Martínez AT, Covert SF, Blanchette RA, Cullen D
Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood.
PLoS Genet. 2014 Dec;10(12):e1004759. doi: 10.1371/journal.pgen.1004759
Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Dueñas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutiérrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kües U, Berka RM, Martínez AT, Covert SF, Blanchette RA, Cullen D
Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood.
PLoS Genet. 2014 Dec;10(12):e1004759. doi: 10.1371/journal.pgen.1004759
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
